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Merge branch 'master' into reconnection

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Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
This commit is contained in:
Grzegorz Kowal 2021-10-26 09:32:49 -03:00
commit c098ae663a
8 changed files with 202 additions and 155 deletions
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10
sources/boundaries.F90
View File

@ -5333,8 +5333,8 @@ module boundaries
use equations , only : csnd2
use gravity , only : gravitational_acceleration
use iso_fortran_env, only : error_unit
use user_problem , only : boundary_user_x, boundary_user_y &
, boundary_user_z
use user_problem , only : user_boundary_x, user_boundary_y &
, user_boundary_z
! local variables are not implicit by default
!
@ -5535,7 +5535,7 @@ module boundaries
!
case(bnd_user)
call boundary_user_x(side(1), jl, ju, kl, ku &
call user_boundary_x(side(1), jl, ju, kl, ku &
, t, dt, x(:), y(:), z(:), qn(:,:,:,:))
! wrong boundary conditions
@ -5713,7 +5713,7 @@ module boundaries
!
case(bnd_user)
call boundary_user_y(side(2), il, iu, kl, ku &
call user_boundary_y(side(2), il, iu, kl, ku &
, t, dt, x(:), y(:), z(:), qn(:,:,:,:))
! wrong boundary conditions
@ -5887,7 +5887,7 @@ module boundaries
!
case(bnd_user)
call boundary_user_z(side(3), il, iu, jl, ju &
call user_boundary_z(side(3), il, iu, jl, ju &
, t, dt, x(:), y(:), z(:), qn(:,:,:,:))
! wrong boundary conditions

5
sources/driver.F90
View File

@ -86,6 +86,7 @@ program amun
use timers , only : start_timer, stop_timer, set_timer, get_timer
use timers , only : get_timer_total, timer_enabled, timer_description
use timers , only : get_count, ntimers
use user_problem , only : user_time_statistics
! module variables are not implicit by default
!
@ -564,6 +565,7 @@ program amun
if (.not. restart_from_snapshot()) then
call store_integrals()
call user_time_statistics()
call write_snapshot()
end if
@ -655,9 +657,10 @@ program amun
!
call store_mesh_stats(step, time)
! store integrals
! store time statistics
!
call store_integrals()
call user_time_statistics()
! write down the restart snapshot
!

44
sources/evolution.F90
View File

@ -350,12 +350,13 @@ module evolution
cfl = 2.5d+00 * cfl
name_int = "Optimized 3ʳᵈ-order 5-step embedded RK3(2)5"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.300285062878154351930669430512780706d-01, &
4.050049049262914975700372321130661410d-01, &
8.947823877926760224705450466361360720d-01, &
7.235108137218888081489570284485201518d-01 ]
7.235108137218888081489570284485201518d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
3.407687209321455242558804921815861422d-01, &
3.414399280584625023244387687873774697d-01, &
@ -415,12 +416,13 @@ module evolution
cfl = 2.5d+00 * cfl
name_int = "Optimized 3ʳᵈ-order 5-step embedded RK3(2)5 FSAL"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.300298624518076223899418286314123354d-01, &
4.050046072094990912268498160116125481d-01, &
8.947822893693433545220710894560512805d-01, &
7.235136928826589010272834603680114769d-01 ]
7.235136928826589010272834603680114769d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
3.407655879334525365094815965895763636d-01, &
3.414382655003386206551709871126405331d-01, &
@ -479,7 +481,7 @@ module evolution
cfl = 3.5d+00 * cfl
name_int = "Optimized 4ᵗʰ-order 9-step embedded RK4(3)9"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.836343531977826022543660465926414772d-01, &
5.484073767552486705240014599676811834d-01, &
@ -488,7 +490,8 @@ module evolution
3.518526451892056368706593492732753284d-01, &
1.665941920204672094647868254892387293d+00, &
9.715276989307335935187466054546761665d-01, &
9.051569554420045339601721625247585643d-01 ]
9.051569554420045339601721625247585643d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
1.262923854387806460989545005598562667d+00, &
7.574967177560872438940839460448329992d-01, &
@ -572,7 +575,7 @@ module evolution
cfl = 3.5d+00 * cfl
name_int = "Optimized 4ᵗʰ-order 9-step embedded RK4(3)9 FSAL"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.836343005184365275160654678626695428d-01, &
5.484076570002894365286665352032296535d-01, &
@ -581,7 +584,8 @@ module evolution
3.518526124230705801739919476290327750d-01, &
1.665941994879593315477304663913129942d+00, &
9.715279295934715835299192116436237065d-01, &
9.051569840159589594903399929316959062d-01 ]
9.051569840159589594903399929316959062d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
1.262923876648114432874834923838556100d+00, &
7.574967189685911558308119415539596711d-01, &
@ -664,7 +668,7 @@ module evolution
cfl = 4.2d+00 * cfl
name_int = "Optimized 5ᵗʰ-order 10-step embedded RK5(4)10"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.597883575710995826783320802193635406d-01, &
9.904573115730917688557891428202061598d-02, &
@ -674,7 +678,8 @@ module evolution
5.449986973408778242805929551952000165d-01, &
7.615224662599497796472095353126697300d-01, &
8.427062083059167761623893618875787414d-01, &
9.152209807185253394871325258038753352d-01 ]
9.152209807185253394871325258038753352d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
-1.331778409133849616712007380176762548d-01, &
8.260422785246030254485064732649153253d-01, &
@ -764,7 +769,7 @@ module evolution
cfl = 4.2d+00 * cfl
name_int = "Optimized 5ᵗʰ-order 10-step embedded RK5(4)10 FSAL"
allocate(c(stages), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
allocate(c(stages+1), dl(stages), bt(stages), bh(stages+1), gm(3,stages))
c (:) = [ 0.000000000000000000000000000000000000d+00, &
2.597883554788674084039539165398464630d-01, &
9.904573247592460887087003212056568980d-02, &
@ -774,7 +779,8 @@ module evolution
5.449986978853637084972622392134732553d-01, &
7.615224694532590139829150720490417596d-01, &
8.427062083267360939805493320684741215d-01, &
9.152209805057669959657927210873423883d-01 ]
9.152209805057669959657927210873423883d-01, &
1.000000000000000000000000000000000000d+00 ]
dl(:) = [ 1.000000000000000000000000000000000000d+00, &
-1.331778419508803397033287009506932673d-01, &
8.260422814750207498262063505871077303d-01, &
@ -3217,14 +3223,15 @@ module evolution
pdata => pdata%next
end do
call update_variables(tm, dtm)
dtm = c(2) * dt
call update_variables(time, dtm)
!= remaining stages
!
do i = 2, stages
tm = time + c(i) * dt
dtm = (c(i) - c(i-1)) * dt
dtm = c(i) * dt
tm = time + dtm
pdata => list_data
do while (associated(pdata))
@ -3252,6 +3259,7 @@ module evolution
pdata => pdata%next
end do
dtm = c(i+1) * dt
call update_variables(tm, dtm)
end do ! i = 2, stages
@ -3348,9 +3356,6 @@ module evolution
!= final step: U(n+1) = U(1)
!
dtm = dt
tm = time + dt
pdata => list_data
do while (associated(pdata))
@ -3361,7 +3366,8 @@ module evolution
pdata => pdata%next
end do
call update_variables(tm, dtm)
tm = time + dt
call update_variables(tm, dt)
#ifdef PROFILE
call stop_timer(imu)

8
sources/gravity.F90
View File

@ -103,8 +103,8 @@ module gravity
! include external procedures and variables
!
use parameters , only : get_parameter
use user_problem , only : gravitational_acceleration_user &
, gravity_enabled_user
use user_problem , only : user_gravitational_acceleration &
, user_gravity_enabled
! local variables are not implicit by default
!
@ -152,8 +152,8 @@ module gravity
! in case of other problems, gravity is calculated by user
!
gravitational_acceleration => gravitational_acceleration_user
gravity_enabled = gravity_enabled_user
gravitational_acceleration => user_gravitational_acceleration
gravity_enabled = user_gravity_enabled
end select

4
sources/problems.F90
View File

@ -102,7 +102,7 @@ module problems
subroutine initialize_problems(problem, verbose, status)
use parameters , only : get_parameter
use user_problem, only : initialize_user_problem, setup_problem_user
use user_problem, only : initialize_user_problem, setup_user_problem
implicit none
@ -150,7 +150,7 @@ module problems
setup_problem => setup_problem_tearing
case default
setup_problem => setup_problem_user
setup_problem => setup_user_problem
call initialize_user_problem(problem, verbose, status)

4
sources/shapes.F90
View File

@ -102,7 +102,7 @@ module shapes
! include external procedures and variables
!
use parameters , only : get_parameter
use user_problem, only : update_shapes_user
use user_problem, only : update_user_shapes
! local variables are not implicit by default
!
@ -160,7 +160,7 @@ module shapes
! no shape update
!
case default
update_shapes => update_shapes_user
update_shapes => update_user_shapes
end select

4
sources/sources.F90
View File

@ -330,7 +330,7 @@ module sources
use equations , only : ibx, iby, ibz, ibp
use gravity , only : gravity_enabled, gravitational_acceleration
use operators , only : divergence, gradient, laplace, curl
use user_problem , only : update_sources_user
use user_problem , only : update_user_sources
! local variables are not implicit by default
!
@ -750,7 +750,7 @@ module sources
! add user defined source terms
!
call update_sources_user(pdata, t, dt, du(:,:,:,:))
call update_user_sources(pdata, t, dt, du(:,:,:,:))
#ifdef PROFILE
! stop accounting time for source terms

278
sources/user_problem.F90
View File

@ -76,12 +76,21 @@ module user_problem
! flag indicating if the gravitational source term is enabled
!
logical, save :: gravity_enabled_user = .false.
logical, save :: user_gravity_enabled = .false.
! allocatable arrays for velocity perturbation
!
real(kind=8), dimension(:), allocatable :: kx, ky, kz, ux, uy, uz, ph
! export subroutines
!
private
public :: initialize_user_problem, finalize_user_problem
public :: setup_user_problem, update_user_sources, update_user_shapes
public :: user_gravitational_acceleration, user_gravity_enabled
public :: user_boundary_x, user_boundary_y, user_boundary_z
public :: user_time_statistics
!- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
!
contains
@ -134,7 +143,7 @@ module user_problem
#if NDIMS == 3
real(kind=8) :: thv, tx, ty, tz, tt
#endif /* NDIMS == 3 */
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -411,7 +420,7 @@ module user_problem
! subroutine arguments
!
integer, intent(out) :: status
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -442,7 +451,7 @@ module user_problem
!
!===============================================================================
!
! subroutine SETUP_PROBLEM_USER:
! subroutine SETUP_USER_PROBLEM:
! -----------------------------
!
! Subroutine sets the initial conditions for the user specific problem.
@ -454,7 +463,7 @@ module user_problem
!
!===============================================================================
!
subroutine setup_problem_user(pdata)
subroutine setup_user_problem(pdata)
! include external procedures and variables
!
@ -512,7 +521,7 @@ module user_problem
real(kind=8), dimension(nn) :: zc
#endif /* NDIMS == 3 */
real(kind=8), dimension(3) :: dh
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -878,104 +887,11 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine setup_problem_user
end subroutine setup_user_problem
!
!===============================================================================
!
! subroutine LOG_COSH:
! -------------------
!
! Function calculates the logarithm of the hyperbolic cosine, which is
! the result of the integration of tanh(x). Direct calculation using
! Fortran intrinsic subroutines fails for large values of x, therefore
! the logarithm of cosh is approximated as |x| + log(1/2) for
! |x| > threshold.
!
! Arguments:
!
! x - function argument;
!
!===============================================================================
!
function log_cosh(x) result(y)
! local variables are not implicit by default
!
implicit none
! function arguments
!
real(kind=8), intent(in) :: x
real(kind=8) :: y
! local parameters
!
real(kind=8), parameter :: th = acosh(huge(x)), lh = log(0.5d+00)
!
!-------------------------------------------------------------------------------
!
if (abs(x) < th) then
y = log(cosh(x))
else
y = abs(x) + lh
end if
!-------------------------------------------------------------------------------
!
end function log_cosh
!
!===============================================================================
!
! subroutine UPDATE_SHAPES_USER:
! -----------------------------
!
! Subroutine defines the regions updated by user.
!
! Arguments:
!
! pdata - pointer to the data block structure of the currently initialized
! block;
! time - time at the moment of update;
! dt - time step since the last update;
!
!===============================================================================
!
subroutine update_shapes_user(pdata, time, dt)
! include external procedures and variables
!
use blocks, only : block_data
! local variables are not implicit by default
!
implicit none
! subroutine arguments
!
type(block_data), pointer, intent(inout) :: pdata
real(kind=8) , intent(in) :: time, dt
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
! start accounting time for the shape update
!
call start_timer(ims)
#endif /* PROFILE */
#ifdef PROFILE
! stop accounting time for the shape update
!
call stop_timer(ims)
#endif /* PROFILE */
!-------------------------------------------------------------------------------
!
end subroutine update_shapes_user
!
!===============================================================================
!
! subroutine UPDATE_SOURCES_USER:
! subroutine UPDATE_USER_SOURCES:
! ------------------------------
!
! Subroutine adds the user defined source terms.
@ -988,7 +904,7 @@ module user_problem
!
!===============================================================================
!
subroutine update_sources_user(pdata, t, dt, du)
subroutine update_user_sources(pdata, t, dt, du)
! include external variables
!
@ -1003,7 +919,7 @@ module user_problem
type(block_data), pointer , intent(inout) :: pdata
real(kind=8) , intent(in) :: t, dt
real(kind=8), dimension(:,:,:,:), intent(inout) :: du
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -1020,11 +936,60 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine update_sources_user
end subroutine update_user_sources
!
!===============================================================================
!
! subroutine GRAVITATIONAL_ACCELERATION_USER:
! subroutine UPDATE_USER_SHAPES:
! -----------------------------
!
! Subroutine defines the regions updated by user.
!
! Arguments:
!
! pdata - pointer to the data block structure of the currently initialized
! block;
! time - time at the moment of update;
! dt - time step since the last update;
!
!===============================================================================
!
subroutine update_user_shapes(pdata, time, dt)
! include external procedures and variables
!
use blocks, only : block_data
! local variables are not implicit by default
!
implicit none
! subroutine arguments
!
type(block_data), pointer, intent(inout) :: pdata
real(kind=8) , intent(in) :: time, dt
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
! start accounting time for the shape update
!
call start_timer(ims)
#endif /* PROFILE */
#ifdef PROFILE
! stop accounting time for the shape update
!
call stop_timer(ims)
#endif /* PROFILE */
!-------------------------------------------------------------------------------
!
end subroutine update_user_shapes
!
!===============================================================================
!
! subroutine USER_GRAVITATIONAL_ACCELERATION:
! ------------------------------------------
!
! Subroutine returns the user defined gravitational acceleration.
@ -1037,7 +1002,7 @@ module user_problem
!
!===============================================================================
!
subroutine gravitational_acceleration_user(t, dt, x, y, z, acc)
subroutine user_gravitational_acceleration(t, dt, x, y, z, acc)
! include external procedures and variables
!
@ -1052,7 +1017,7 @@ module user_problem
real(kind=8) , intent(in) :: t, dt
real(kind=8) , intent(in) :: x, y, z
real(kind=8), dimension(3), intent(out) :: acc
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -1073,11 +1038,11 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine gravitational_acceleration_user
end subroutine user_gravitational_acceleration
!
!===============================================================================
!
! subroutine BOUNDARY_USER_X:
! subroutine USER_BOUNDARY_X:
! --------------------------
!
! Subroutine updates ghost zones within the specific region along
@ -1094,7 +1059,7 @@ module user_problem
!
!===============================================================================
!
subroutine boundary_user_x(ic, jl, ju, kl, ku, t, dt, x, y, z, qn)
subroutine user_boundary_x(ic, jl, ju, kl, ku, t, dt, x, y, z, qn)
! import external procedures and variables
!
@ -1131,7 +1096,7 @@ module user_problem
#if NDIMS == 3
real(kind=8) :: dz, dxz
#endif /* NDIMS == 3 */
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -1288,11 +1253,11 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine boundary_user_x
end subroutine user_boundary_x
!
!===============================================================================
!
! subroutine BOUNDARY_USER_Y:
! subroutine USER_BOUNDARY_Y:
! --------------------------
!
! Subroutine updates ghost zones within the specific region along
@ -1309,7 +1274,7 @@ module user_problem
!
!===============================================================================
!
subroutine boundary_user_y(jc, il, iu, kl, ku, t, dt, x, y, z, qn)
subroutine user_boundary_y(jc, il, iu, kl, ku, t, dt, x, y, z, qn)
! import external procedures and variables
!
@ -1345,7 +1310,7 @@ module user_problem
real(kind=8) :: dz, dyz
#endif /* NDIMS == 3 */
real(kind=8) :: fl, fr
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -1515,11 +1480,11 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine boundary_user_y
end subroutine user_boundary_y
!
!===============================================================================
!
! subroutine BOUNDARY_USER_Z:
! subroutine USER_BOUNDARY_Z:
! --------------------------
!
! Subroutine updates ghost zones within the specific region along
@ -1536,7 +1501,7 @@ module user_problem
!
!===============================================================================
!
subroutine boundary_user_z(kc, il, iu, jl, ju, t, dt, x, y, z, qn)
subroutine user_boundary_z(kc, il, iu, jl, ju, t, dt, x, y, z, qn)
! local variables are not implicit by default
!
@ -1552,7 +1517,7 @@ module user_problem
real(kind=8), dimension(:) , intent(in) :: y
real(kind=8), dimension(:) , intent(in) :: z
real(kind=8), dimension(:,:,:,:), intent(inout) :: qn
!
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
@ -1569,7 +1534,80 @@ module user_problem
!-------------------------------------------------------------------------------
!
end subroutine boundary_user_z
end subroutine user_boundary_z
!
!===============================================================================
!
! subroutine USER_TIME_STATISTICS:
! -------------------------------
!
! Subroutine can be use to store user defined time statistics. The file to
! store these statistics should be properly created in subroutine
! initialize_user_problem() and closed in finalize_user_problem().
!
!===============================================================================
!
subroutine user_time_statistics()
implicit none
!-------------------------------------------------------------------------------
!
#ifdef PROFILE
call start_timer(imt)
#endif /* PROFILE */
#ifdef PROFILE
call stop_timer(imt)
#endif /* PROFILE */
!-------------------------------------------------------------------------------
!
end subroutine user_time_statistics
!
!===============================================================================
!
! subroutine LOG_COSH:
! -------------------
!
! Function calculates the logarithm of the hyperbolic cosine, which is
! the result of the integration of tanh(x). Direct calculation using
! Fortran intrinsic subroutines fails for large values of x, therefore
! the logarithm of cosh is approximated as |x| + log(1/2) for
! |x| > threshold.
!
! Arguments:
!
! x - function argument;
!
!===============================================================================
!
function log_cosh(x) result(y)
! local variables are not implicit by default
!
implicit none
! function arguments
!
real(kind=8), intent(in) :: x
real(kind=8) :: y
! local parameters
!
real(kind=8), parameter :: th = acosh(huge(x)), lh = log(0.5d+00)
!-------------------------------------------------------------------------------
!
if (abs(x) < th) then
y = log(cosh(x))
else
y = abs(x) + lh
end if
!-------------------------------------------------------------------------------
!
end function log_cosh
!===============================================================================
!